diff --git a/editor/docks/filesystem_dock.cpp b/editor/docks/filesystem_dock.cpp
index 529786c5e70..020d37b4701 100644
--- a/editor/docks/filesystem_dock.cpp
+++ b/editor/docks/filesystem_dock.cpp
@@ -1925,6 +1925,8 @@ void FileSystemDock::_convert_dialog_action() {
 		Ref<Resource> original_resource = selected_resources.get(i);
 		Ref<Resource> new_resource = converted_resources.get(i);
 
+		// Notify plugins that the original resource is removed.
+		emit_signal(SNAME("file_removed"), original_resource->get_path());
 		// Overwrite the path.
 		new_resource->set_path(original_resource->get_path(), true);
 
diff --git a/editor/inspector/editor_resource_picker.cpp b/editor/inspector/editor_resource_picker.cpp
index 141c05498eb..8a4ea9d6e9b 100644
--- a/editor/inspector/editor_resource_picker.cpp
+++ b/editor/inspector/editor_resource_picker.cpp
@@ -484,8 +484,11 @@ void EditorResourcePicker::_edit_menu_cbk(int p_which) {
 				Vector<Ref<EditorResourceConversionPlugin>> conversions = EditorNode::get_singleton()->find_resource_conversion_plugin_for_resource(edited_resource);
 				ERR_FAIL_INDEX(to_type, conversions.size());
 
-				edited_resource = conversions[to_type]->convert(edited_resource);
-				_resource_changed();
+				Ref<Resource> converted_resource = conversions[to_type]->convert(edited_resource);
+				if (converted_resource.is_valid()) {
+					edited_resource = converted_resource;
+					_resource_changed();
+				}
 				break;
 			}
 
diff --git a/editor/shader/visual_shader_editor_plugin.cpp b/editor/shader/visual_shader_editor_plugin.cpp
index 33b6088a112..bb6562a9b17 100644
--- a/editor/shader/visual_shader_editor_plugin.cpp
+++ b/editor/shader/visual_shader_editor_plugin.cpp
@@ -41,6 +41,7 @@
 #include "editor/editor_string_names.h"
 #include "editor/editor_undo_redo_manager.h"
 #include "editor/file_system/editor_paths.h"
+#include "editor/gui/editor_toaster.h"
 #include "editor/inspector/editor_properties.h"
 #include "editor/inspector/editor_properties_vector.h"
 #include "editor/scene/curve_editor_plugin.h"
@@ -8446,6 +8447,20 @@ bool VisualShaderConversionPlugin::handles(const Ref<Resource> &p_resource) cons
 Ref<Resource> VisualShaderConversionPlugin::convert(const Ref<Resource> &p_resource) const {
 	Ref<VisualShader> vshader = p_resource;
 	ERR_FAIL_COND_V(vshader.is_null(), Ref<Resource>());
+	int embed = vshader->has_node_embeds();
+
+	EditorToaster *toast = EditorToaster::get_singleton();
+	if (toast == nullptr) {
+		ERR_FAIL_COND_V_MSG(embed == 2, Ref<Resource>(), "Cannot convert VisualShader to GDShader because VisualShader has embedded subresources.");
+		if (embed == 1) {
+			WARN_PRINT("Visual Shader conversion cannot convert external dependencies. Resource references from Nodes will have to be rebound as ShaderParameters on a Material.");
+		}
+	} else if (embed == 2) {
+		toast->popup_str(TTR("Cannot convert VisualShader to GDShader because VisualShader has embedded subresources."), EditorToaster::SEVERITY_ERROR);
+		return Ref<Resource>();
+	} else if (embed == 1) {
+		toast->popup_str(TTR("Visual Shader conversion cannot convert external dependencies. Resource references from Nodes will have to be rebound as ShaderParameters on a Material."), EditorToaster::SEVERITY_WARNING);
+	}
 
 	Ref<Shader> shader;
 	shader.instantiate();
diff --git a/scene/resources/visual_shader.cpp b/scene/resources/visual_shader.cpp
index cd5ce0a6657..a2abb10d7a4 100644
--- a/scene/resources/visual_shader.cpp
+++ b/scene/resources/visual_shader.cpp
@@ -967,6 +967,37 @@ void VisualShader::set_node_position(Type p_type, int p_id, const Vector2 &p_pos
 	g->nodes[p_id].position = p_position;
 }
 
+// Returns 0 if no embeds, 1 if external embeds, 2 if builtin embeds
+int VisualShader::has_node_embeds() const {
+	bool external_embeds = false;
+	for (int i = 0; i < TYPE_MAX; i++) {
+		for (const KeyValue<int, Node> &E : graph[i].nodes) {
+			List<PropertyInfo> props;
+			E.value.node->get_property_list(&props);
+			// For classes that inherit from VisualShaderNode, the class properties start at the 12th, and the last value is always 'script'
+			for (int j = 12; j < props.size() - 1; j++) {
+				// VisualShaderNodeCustom cannot have embeds
+				if (props.get(j).name == "VisualShaderNodeCustom") {
+					break;
+				}
+				// Ref<Resource> properties get classed as type Variant::Object
+				if (props.get(j).type == Variant::OBJECT) {
+					Ref<Resource> res = E.value.node->get(props.get(j).name);
+					if (res.is_valid()) {
+						if (res->is_built_in()) {
+							return 2;
+						} else {
+							external_embeds = true;
+						}
+					}
+				}
+			}
+		}
+	}
+
+	return external_embeds;
+}
+
 Vector2 VisualShader::get_node_position(Type p_type, int p_id) const {
 	ERR_FAIL_INDEX_V(p_type, TYPE_MAX, Vector2());
 	const Graph *g = &graph[p_type];
diff --git a/scene/resources/visual_shader.h b/scene/resources/visual_shader.h
index 6ca86c7b47b..5e707092f21 100644
--- a/scene/resources/visual_shader.h
+++ b/scene/resources/visual_shader.h
@@ -183,6 +183,7 @@ public: // internal methods
 
 	void add_node(Type p_type, const Ref<VisualShaderNode> &p_node, const Vector2 &p_position, int p_id);
 	void set_node_position(Type p_type, int p_id, const Vector2 &p_position);
+	int has_node_embeds() const;
 
 	void add_varying(const String &p_name, VaryingMode p_mode, VaryingType p_type);
 	void remove_varying(const String &p_name);